text stringlengths 1 93.6k |
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def load_pkl(pkl):
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with open(pkl, "rb") as f:
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x = pickle.load(f)
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return x
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def save_pkl(data, out_pkl, mode="wb"):
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if mode == "wb" and os.path.exists(out_pkl):
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vlog(f"Warning: {out_pkl} already exists. Overwriting.")
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with open(out_pkl, mode) as f:
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pickle.dump(data, f)
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def R_from_eman(a, b, y):
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a *= np.pi / 180.0
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b *= np.pi / 180.0
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y *= np.pi / 180.0
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ca, sa = np.cos(a), np.sin(a)
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cb, sb = np.cos(b), np.sin(b)
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cy, sy = np.cos(y), np.sin(y)
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Ra = np.array([[ca, -sa, 0], [sa, ca, 0], [0, 0, 1]])
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Rb = np.array([[1, 0, 0], [0, cb, -sb], [0, sb, cb]])
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Ry = np.array(([cy, -sy, 0], [sy, cy, 0], [0, 0, 1]))
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R = np.dot(np.dot(Ry, Rb), Ra)
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# handling EMAN convention mismatch for where the origin of an image is (bottom right vs top right)
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R[0, 1] *= -1
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R[1, 0] *= -1
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R[1, 2] *= -1
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R[2, 1] *= -1
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return R
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def R_from_relion(a, b, y):
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a *= np.pi / 180.0
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b *= np.pi / 180.0
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y *= np.pi / 180.0
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ca, sa = np.cos(a), np.sin(a)
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cb, sb = np.cos(b), np.sin(b)
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cy, sy = np.cos(y), np.sin(y)
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Ra = np.array([[ca, -sa, 0], [sa, ca, 0], [0, 0, 1]])
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Rb = np.array([[cb, 0, -sb], [0, 1, 0], [sb, 0, cb]])
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Ry = np.array(([cy, -sy, 0], [sy, cy, 0], [0, 0, 1]))
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R = np.dot(np.dot(Ry, Rb), Ra)
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R[0, 1] *= -1
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R[1, 0] *= -1
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R[1, 2] *= -1
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R[2, 1] *= -1
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return R
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def R_from_relion_scipy(euler_, degrees=True):
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"""Nx3 array of RELION euler angles to rotation matrix"""
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from scipy.spatial.transform import Rotation as RR
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euler = euler_.copy()
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if euler.shape == (3,):
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euler = euler.reshape(1, 3)
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euler[:, 0] += 90
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euler[:, 2] -= 90
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f = np.ones((3, 3))
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f[0, 1] = -1
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f[1, 0] = -1
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f[1, 2] = -1
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f[2, 1] = -1
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rot = RR.from_euler("zxz", euler, degrees=degrees).as_matrix() * f
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return rot
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def R_to_relion_scipy(rot, degrees=True):
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"""Nx3x3 rotation matrices to RELION euler angles"""
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from scipy.spatial.transform import Rotation as RR
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if rot.shape == (3, 3):
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rot = rot.reshape(1, 3, 3)
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assert len(rot.shape) == 3, "Input must have dim Nx3x3"
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f = np.ones((3, 3))
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f[0, 1] = -1
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f[1, 0] = -1
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f[1, 2] = -1
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f[2, 1] = -1
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euler = RR.from_matrix(rot * f).as_euler("zxz", degrees=True)
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euler[:, 0] -= 90
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euler[:, 2] += 90
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euler += 180
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euler %= 360
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euler -= 180
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if not degrees:
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euler *= np.pi / 180
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return euler
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def xrot(tilt_deg):
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"""Return rotation matrix associated with rotation over the x-axis"""
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theta = tilt_deg * np.pi / 180
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tilt = np.array(
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[
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[1.0, 0.0, 0.0],
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[0, np.cos(theta), -np.sin(theta)],
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[0, np.sin(theta), np.cos(theta)],
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]
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